Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation.

Area of Science:

• Epigenetics and chromatin biology
• Molecular mechanisms of DNA methylation
• Genome stability

Background:

• Functional crosstalk between DNA methylation, H3K9me3, and HP1 is crucial for heterochromatin assembly and genome stability.
• Mechanisms guiding DNA methyltransferases to specific genomic regions by repressive chromatin cues are not well understood.

Purpose of the Study:

• To characterize the structure-function of the DNA methyltransferase DIM2 in Neurospora.
• To elucidate how DIM2 interacts with H3K9me3 and HP1 to mediate DNA methylation.
• To uncover the distinct substrate-binding mechanism of DIM2 compared to mammalian DNMT1.

Main Methods:

• Structure-function characterizations of DIM2.
• X-ray crystallography to determine the structures of DIM2-HP1 and DIM2-HP1-H3K9me3-DNA complexes.
• Biochemical assays to assess DNA methylation activity and substrate binding.

Main Results:

• DIM2 DNA methylation activity strictly requires both H3K9me3 and HP1.
• A bipartite DIM2-HP1 interaction induces a disorder-to-order transition in DIM2's target-recognition domain, enabling substrate binding.
• The DIM2-HP1-H3K9me3-DNA complex structure reveals a unique substrate-binding mechanism.
• Dual recognition of H3K9me3 by DIM2's RFTS and BAH1 domains allosterically regulates DIM2-substrate binding and methylation activity.

Conclusions:

• Multiple heterochromatin factors (H3K9me3, HP1) coordinate to control DIM2 activity.
• DIM2 employs a novel mechanism for region-specific DNA methylation, distinct from mammalian orthologues.
• This study provides insights into the regulation of heterochromatin formation and genome stability.